Hi, a small addition to Mark's answer. If you want/need to use an older gcc version 4.4.6 and 4.5.3 have the necessary fix too. Also you can disable AVX with cmake -DGMX_CPU_ACCELERATION=SSE4.1 . But you will get somewhat lower performance (AFAIK only 10% with group kernels but more with verlet kernels). If you want to track the status of the this Gromacs bug you can find it here: http://redmine.gromacs.org/issues/1058
Roland On Mon, Dec 3, 2012 at 4:43 PM, Mark Abraham <[email protected]>wrote: > Looks like a compiler bug to me, and google agrees > http://gcc.gnu.org/bugzilla/show_bug.cgi?id=47318. > > Even if there were not this bug, we would strongly encourage you to get the > better performance available from more recent versions of gcc. I was about > to suggest 4.6 or newer, but the above URL suggests 4.6.0 has the same bug > :-O. So go higher than that, or Intel's compiler. > > We will probably try detecting this at configure time in a future beta. > Clearly our test matrix doesn't cover this case, but as Szilard has > mentioned in another thread, the multiplicative explosion of possibilities > for us to try to anticipate to make users' lives easier during installation > makes our lives pretty tough :-) > > Mark > > On Mon, Dec 3, 2012 at 8:05 PM, sebastian < > [email protected]> wrote: > > > Hey Dear, > > > > when I try to install the GROMACS-4.6-beta1 version I get an error which > I > > can not pin down when do make. > > > > My system: > > > > CPU: i7 > > GPU: NVIDIA GTX670 > > gcc: Debian 4.4.5-8 > > CUDA: 4.2 > > fft3w: 3.3.2 including sse2 > > Debian Linux 64-bit > > > > First I do: > > > > cmake ../ -DCMAKE_INSTALL_PREFIX=/usr/**local/gromacs_4.6 > > > > which works fine. When I do: > > > > make -j6 > > > > I get a bunch of errors which look more or less the same: > > > > gromacs-4.6-beta1/src/gmxlib/**nonbonded/nb_kernel_avx_256_** > > single/kernelutil_x86_avx_256_**single.h:600: error: incompatible type > > for argument 2 of ‘_mm_maskload_ps’ > > /usr/lib/gcc/x86_64-linux-gnu/**4.4.5/include/avxintrin.h:919: note: > > expected ‘__m128’ but argument is of type ‘__m128i’ > > > > or like: > > > > gromacs-4.6-beta1/src/gmxlib/**nonbonded/nb_kernel_avx_256_** > > single/kernelutil_x86_avx_256_**single.h:607: error: incompatible type > > for argument 2 of ‘_mm_maskstore_ps’ > > /usr/lib/gcc/x86_64-linux-gnu/**4.4.5/include/avxintrin.h:926: note: > > expected ‘__m128’ but argument is of type ‘__m128i’ > > > > and it breaks with this output: > > > > make[2]: *** [src/gmxlib/CMakeFiles/gmx.**dir/nonbonded/nb_kernel_avx_** > > 256_single/nb_kernel_ElecCoul_**VdwCSTab_GeomW4W4_avx_256_**single.c.o] > > Error 1 > > make[1]: *** [src/gmxlib/CMakeFiles/gmx.**dir/all] Error 2 > > make: *** [all] Error 2 > > > > I don't know what goes wrong and maybe I just miss a flag. > > > > Dears, > > > > Sebastian > > > > -- > > gmx-users mailing list [email protected] > > http://lists.gromacs.org/**mailman/listinfo/gmx-users< > http://lists.gromacs.org/mailman/listinfo/gmx-users> > > * Please search the archive at http://www.gromacs.org/** > > Support/Mailing_Lists/Search< > http://www.gromacs.org/Support/Mailing_Lists/Search>before posting! > > * Please don't post (un)subscribe requests to the list. Use the www > > interface or send it to [email protected]. > > * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists< > http://www.gromacs.org/Support/Mailing_Lists> > > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
